Waking up in a strange bedroom in a dream world, teenager Haruto Tsukishiro finds a strange app on his phone. When he activates the program, an odd woman appears and tries to drag him to her realm. Luckily, a mysterious, white-haired girl severs their connection and helps him escape, revealing that the woman is a witch; however, their conversation is cut short. As Haruto enters the realm again, he meets an anthropomorphic, talking cat named Katsumi Kanzaki. While the witch's minions pursue them, the white-haired girl opens a door for them to escape. After their ordeal, Haruto describes their savior—which only he can see—and Katsumi, the leading authority on dream world research, realizes that she must be Lily, a being that resurfaces repeatedly across multiple dreamscapes. Hoping to leave the dream world through a blue door, they enter the witch's realm once again. Finding themselves in peril, Lily reveals the truth to Haruto: witches suffer from Sleeping Beauty Syndrome, a coma-like sleep state induced by torment in their real world lives. Thus, they cannot wake until they are defeated in the dream world. After finally defeating the witch and locating the blue door, Haruto and Katsumi say their farewells, promising to meet up in the real world. However, when Haruto exits through the door, he awakens in the dream world bedroom once more. Seeking answers, Haruto and Katsumi try to uncover the mysteries of the witches, Lily, and Haruto's own inability to leave the dream world.

For Hikari Tsutsui, life within the two-dimensional realm is much simpler. Socially inept and awkward, he immerses himself in video games and anime, only to be relentlessly ridiculed and ostracized by his classmates. Sharing his misery is Yuuto Itou, his only friend, who wears cat ears and is equally obsessed with the world of games. After being forced to clean the pool as punishment for arriving late, Tsutsui meets Iroha Igarashi, but he attempts to steer clear of her, as her notoriety precedes her. Brazenly blunt, loathed by female classmates, and infamous for messing around with boys, Tsutsui believes that getting involved with her would cause nothing but problems. 3D Kanojo: Real Girl is a story revolving around these two outcasts—a boy full of emotions he has never experienced before, struggling to lay them bare, and a girl who strives to break him out of his shell.

The spring term is beginning for the students at Lillian Girls' Academy. Friends are reunited, but for the Yamayuri Council, it's a bittersweet time. Yoko, Eriko, and Sei are busy preparing to depart Lillian while Sachiko, Rei, and Shimako are doing their best to ensure that their dear sisters receive a memorable commencement. Sei's departure will leave a sizable hole in the White Roses, and filling it won't be easy. But is there anyone who could appeal to Shimako enough to become the next Rosa Gigantea en bouton? (Source: RightStuf)

In 2029, a large scale ground sinkage occurred in the Mediterranean Sea. Chemical elements such as oxygen, carbon, gold, molybdenum, and cobalt disappeared from the earth's crust suddenly. The human population was decreased by 90% in sixty years. Researchers found out that the disappeared elements were drained into a planet Nega Earth, located in another dimension. To save the Earth, a special team called the Element Hunters is organized. All of the members are under 13 years old, because young and flexible brains are needed to access Nega Earth.